TL;DR
The results demonstrate that path-metadynamics enables the calculation of rate constants, the localization of transition states, and the mapping of the free energy along a transition path described on a high-dimensional space.
It is shown that the PMD enhanced sampling approach in combination with force-field MD simulations of conformational transitions that require three or more collective variables (CVs) to describe the processes efficiently localizes the average transition path and simultaneously obtains the free-energy profile along the...
This work employs MD simulations and the path-metadynamics method to elucidate the dissociation/formation mechanism of the complex GCN4 leucine zipper between the native state (N) and the denatured state (D).
It is demonstrated that BioEmu can generate plausible conformational ensembles for relatively large, six-and seven-pass membrane proteins, sampling rare states at a fraction of the computational cost of conventional MD simulations, suggesting that AI-based ensemble generation could provide an accessible approach for ex...
Gen-COMPAS is introduced, a generative committor-guided path-sampling framework that reconstructs rare biomolecular transition pathways and reveals the underlying thermodynamics and kinetics without using predefined collective variables or brute-force sampling, at an acceptable computational cost.
Mechanically interlocked molecules, such as rotaxanes and catenanes, display complex internal dynamics and reciprocal motions that are central to their use as artificial molecular machines. Revealing how these motions occur, the key interactions, and the rate-limiting steps determining their kinetics is essential for u...
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